A hierarchical modulation joint-physical layer network coding scheme is proposed to address the problems of incomplete channel condition utilization in asymmetric cooperative free space optical communication system and deterioration of data reliability due to high-order modulation. In this scheme, the information to be transmitted is classified first in data priorities at the source node followed by the allocation of transmission powers of different proportions to the prioritized data. Subsequently, the modulated data are sent to each node, and physical layer network coding is performed on the received data at the relay node. Finally, the relay node sends the encoded information to the destination node, and the destination node recovers the original information using the physical layer network coding scheme. The simulation results show that the bit error rate (BER) of the system can be reduced to values < 10^-8 in high-signal-to-noise ratio (SNR) channels. The system can achieve SNR gains ≥1.5 dB by using this scheme in the intense atmospheric turbulence channel. This scheme yields better antijamming performance in intense atmospheric turbulence channel cases.